OK, sorry, I wasn’t sure about your level of knowledge in terms of the structure behind the project and such. Let me try another approach.

RetroPie is basically a collection of scripts (automation) to setup a the Raspbian OS on your Pi so that it runs EmulationStation and a couple of emulators (plus a couple of handy enhancements).

The setup script either installs the emulators via binary distribution (someone else already compiled the source code and you just get the resulting “program”) or source distribution (the script downloads the source code, compiles it, copies the “program” to a folder and deletes the source from your Pi). Either way as a user you actually never “see” the source-code on your Pi because it either never made it there or was deleted after generating the emulator from it.

What you would have to do is manually getting the source-code you would like to edit (like the setup script does), change it and then compile it. What I was suggesting was mimicking what the setup script does (this is on your Pi in /home/pi/RetroPie-Setup), if you have never had any contact with bash scripts before this might be too much of a hurdle though.

Is the change you would like to have implemented already don by the authors of PocketSNES? If so it would suffice to just let the setup script compile a new version for you.

What you would need to do for this, is first update the setup script:

cd
cd RetroPie-Setup
sudo ./retropie_setup.sh
<Update Script>
<Reboot>

Then update the PocketSNES emulator from source by executing the setup script like before and choosing to update “individual emulators” and then “from source”.

Hope this made some sense…